Locus 5739

Sequence ID 3L_DroMel_CAF1
Location 15,611,056 – 15,611,215
Length 159
Max. P 0.911249
window9097 window9098 window9099

overview

Window 7

Location 15,611,056 – 15,611,175
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.48
Mean single sequence MFE -31.64
Consensus MFE -27.28
Energy contribution -27.76
Covariance contribution 0.48
Combinations/Pair 1.03
Mean z-score -1.57
Structure conservation index 0.86
SVM decision value 1.08
SVM RNA-class probability 0.911249
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15611056 119 - 23771897
CUGAUACCAUAGUUGAGCCAU-UGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUAUGUUACGCCCAUUUGAGUGUGCAAAAUUGUGUUUAACUAAAACCGAUGAC
.........((((((((((((-((((......))))).(((.....)))..(..(((.(((((.((((........))))))))).)))..).....)).)))))))))........... ( -31.50)
>DroSec_CAF1 34157 119 - 1
CUGAUACCAUAGUUGAGCCAU-UGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUAUGUUACGCCCAUUUGAGUGUGCAAAAUUGUGUUUAACGAAAAUCGAUGAC
...........(((((....(-(((...(((((((((.(((.....)))..(..(((.(((((.((((........))))))))).)))..)....)))))))))))))...)))))... ( -31.60)
>DroSim_CAF1 34169 119 - 1
CUGAUACCAUAGUUGAGCCAU-UGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUAUGUUACGCCCAUUUGAGUGUGCAAAAUUGUGUUUAACGAAAACCGAUGAC
............(((((((.(-((((......)))))......))))))).(..(((.(((((.((((........))))))))).)))..)...((((.((((.....))))))))... ( -30.50)
>DroEre_CAF1 34222 119 - 1
CUGAUACCAAAGUUGAGCCAUUUGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUGUGUUACGCCCAUUUGGCUGGGCAAAAUUGUGUUUAACUAAG-GCGAAGAC
......((..((((((((((((((((......))))))))...........((.((..(((((.((((........)))))))))..)).))........))))))))..)-)....... ( -31.10)
>DroYak_CAF1 36485 119 - 1
CUGAUACCACAGUUGAGCCAUUUGUGAGUAAGCACAGAUGAUAGGUUCGGAGUGCACAUAAAUAGGACUCUGUUACGCCCAUUUGGGUGUGCAAAAUUGUGUUUAACUAAA-GCGAUGAA
.......(((((((..((((((((((......)))))))).......((((((.(.........).))))))..((((((....))))))))..)))))))..........-........ ( -33.50)
>consensus
CUGAUACCAUAGUUGAGCCAU_UGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUAUGUUACGCCCAUUUGAGUGUGCAAAAUUGUGUUUAACUAAAACCGAUGAC
.......((((((((((((((.((((......))))....)).)))))...(..(((.(((((.((((........))))))))).)))..)..)))))))................... (-27.28 = -27.76 +   0.48)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,611,096 – 15,611,215
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 95.49
Mean single sequence MFE -27.98
Consensus MFE -25.80
Energy contribution -25.68
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -1.14
Structure conservation index 0.92
SVM decision value 0.15
SVM RNA-class probability 0.606087
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15611096 119 + 23771897
GGGCGUAACAUAGCCCUAUUUAUGUGCACUUUGAACCUAUCAUCUGUGCUUACUCACA-AUGGCUCAACUAUGGUAUCAGUUGUUAAGUUGAAAUGCCAGGACACAAAAGCACACCAAAA
((((........))))......(((((..((((..(((......((((......))))-..(((((((((.(..((.....))..)))))))...))))))...)))).)))))...... ( -28.90)
>DroSec_CAF1 34197 119 + 1
GGGCGUAACAUAGCCCUAUUUAUGUGCACUUUGAACCUAUCAUCUGUGCUUACUCACA-AUGGCUCAACUAUGGUAUCAGUUGUUAGGUUGAAAUGCCAGGACACAAAAGCAUACCAAAA
((((........))))....((((((((.(((.((((((.((.(((....((((....-((((.....)))))))).))).)).)))))).))))))..(....)....)))))...... ( -27.60)
>DroSim_CAF1 34209 119 + 1
GGGCGUAACAUAGCCCUAUUUAUGUGCACUUUGAACCUAUCAUCUGUGCUUACUCACA-AUGGCUCAACUAUGGUAUCAGUUGUUAAGUUGAAAUGCCAGGACACAAAAGCAUACCAAAA
((((........))))....(((((((((..(((.....)))...))))....((...-.((((((((((.(..((.....))..)))))))...)))).)).......)))))...... ( -27.70)
>DroEre_CAF1 34261 120 + 1
GGGCGUAACACAGCCCUAUUUAUGUGCACUUUGAACCUAUCAUCUGUGCUUACUCACAAAUGGCUCAACUUUGGUAUCAGUUGUUAAGUGGAAAGGCCAGGACACAAAAGCACACCAAAA
((((........))))......(((((....(((.....)))((((.((((..((((.((..(((..((....))...)))..))..))))..))))))))........)))))...... ( -29.30)
>DroYak_CAF1 36524 120 + 1
GGGCGUAACAGAGUCCUAUUUAUGUGCACUCCGAACCUAUCAUCUGUGCUUACUCACAAAUGGCUCAACUGUGGUAUCAGUUGUUAAGUUGAAAUGCCAGGACACAAGAGCACACCAAAA
((((........))))......(((((.((.....(((......((((......))))...(((.((((((......))))))............)))))).....)).)))))...... ( -26.42)
>consensus
GGGCGUAACAUAGCCCUAUUUAUGUGCACUUUGAACCUAUCAUCUGUGCUUACUCACA_AUGGCUCAACUAUGGUAUCAGUUGUUAAGUUGAAAUGCCAGGACACAAAAGCACACCAAAA
((((........))))......(((((..((((..(((......((((......))))...(((((((((.(..((.....))..)))))))...))))))...)))).)))))...... (-25.80 = -25.68 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,611,096 – 15,611,215
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.49
Mean single sequence MFE -33.26
Consensus MFE -27.93
Energy contribution -28.13
Covariance contribution 0.20
Combinations/Pair 1.11
Mean z-score -1.57
Structure conservation index 0.84
SVM decision value 0.61
SVM RNA-class probability 0.798607
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15611096 119 - 23771897
UUUUGGUGUGCUUUUGUGUCCUGGCAUUUCAACUUAACAACUGAUACCAUAGUUGAGCCAU-UGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUAUGUUACGCCC
.....(((((((((((...((((((...((((((................))))))))).(-((((......))))).....)))..))))).)))))).....((((........)))) ( -32.59)
>DroSec_CAF1 34197 119 - 1
UUUUGGUAUGCUUUUGUGUCCUGGCAUUUCAACCUAACAACUGAUACCAUAGUUGAGCCAU-UGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUAUGUUACGCCC
....((.((((....))))))((((((((.((((((.((.(((.(((((((((......))-)))).)))....))).)).))))))..)))))).))......((((........)))) ( -29.70)
>DroSim_CAF1 34209 119 - 1
UUUUGGUAUGCUUUUGUGUCCUGGCAUUUCAACUUAACAACUGAUACCAUAGUUGAGCCAU-UGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUAUGUUACGCCC
....((.((((....))))))((((((((.((((((.((.(((.(((((((((......))-)))).)))....))).)).))))))..)))))).))......((((........)))) ( -27.00)
>DroEre_CAF1 34261 120 - 1
UUUUGGUGUGCUUUUGUGUCCUGGCCUUUCCACUUAACAACUGAUACCAAAGUUGAGCCAUUUGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUGUGUUACGCCC
.....(((((((((((...((((..............(((((........)))))...((((((((......)))))))).))))..))))).)))))).....((((........)))) ( -35.60)
>DroYak_CAF1 36524 120 - 1
UUUUGGUGUGCUCUUGUGUCCUGGCAUUUCAACUUAACAACUGAUACCACAGUUGAGCCAUUUGUGAGUAAGCACAGAUGAUAGGUUCGGAGUGCACAUAAAUAGGACUCUGUUACGCCC
....(((((((....(.(((((((((((((((((((.((((((......))))))...((((((((......)))))))).)))))).))))))).......)))))).).).)))))). ( -41.41)
>consensus
UUUUGGUGUGCUUUUGUGUCCUGGCAUUUCAACUUAACAACUGAUACCAUAGUUGAGCCAU_UGUGAGUAAGCACAGAUGAUAGGUUCAAAGUGCACAUAAAUAGGGCUAUGUUACGCCC
....((((((.......((((((((((((..(((((.((((((......))))))...(((.((((......)))).))).)))))...)))))).......)))))).....)))))). (-27.93 = -28.13 +   0.20)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:22 2006